RetrogeneDB ID: retro_cpor_99

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:23333607..23334777(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000012343
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ZNF234
• Ensembl ID: ENSCPOG00000004610
• Aliases: None
• Description: zinc finger protein 234 [Source:HGNC Symbol;Acc:13027]

Sequence

>retro_cpor_99
CCAGGAAAAGAGAAGTATGACAACCAAGAAGGAAATGTTCAGTCTGTTTCCCCTGAGAACACTCACTCTCAGGTGCTGTT
TCCTGGCCAGGCCAGAGGAGAGGTACCCTGGAGTCCTGAGCAGGGCCAGCCTCATGACAGGGCAGAAGGGCACTGGGAAC
CTCCTCCAGAAGATGAAATGGAGCAGTCCTTAACAGGAGCCACGGGTTGCAGAGAACTGGGGCCACCAAAGGAACTGCAG
CCAAAAAAACTTCATTTATGTCCCTTGTGTGGCAAAAATTTCTCTAATAACTCAAACCTAATTAGACATCAGAGAATACA
TGCAGCAGAAAGACTATGTATGGGTGTGGAGTGCAGTGAAATCTTTGGTGGGCATCCACATTTTCTCTCACTACATAAAG
CACACCTGGGAGAGGAGGCCCATAAGTGCCTAGAGTGTGGGAAATGCTTCAGTCAAAATACCCATCTGACTCGCCATCAG
CGAACCCACACAGGTGAGAAGCCTTATCAGTGCAATGTATGTGGAAAAAGCTTCTCTTGCAACTCCAACCTCCATAGGCA
CCAAAGGACACACACTGGAGAAAAACCCTACAAGTGCTCTGAGTGTGGGGAGATCTTTGCTCACAGCTCCAACCTTCTTA
GACACCAGAGGATCCACACAGGAGAGAGACCCTATAAGTGTGCTGAATGTGGGAAAAGTTTCTCTCGGAGTTCTCACCTT
GTCATTCATGAAAGAACTCATGAGAGAGAGAGACTTGACCCCTTCTCTGAGAATGGGGAGGCCATGAGTGATGGTACTCC
CTTTCTTCCAAGTCAGGGAACCCGCAGAGCAGAAAAGAAACTCTTTGAATGTTCAACTTGTGGTAAAAGCTTCCGGCAGG
GCATGCATCTTACTAGACACCAGAGAACGCACACAGGAGAGAAACCGTACAAATGTACCCTTTGTGGAGAAAATTTCTCT
CATAGATCCAACTTAATCCGGCACCAGAGAATTCACACAGGAGAAAAACCCTATACTTGTCATGAGTGCGGAGACAGTTT
CTCTCACAGCTCCAATCGGATTCGTCACCTGAGAACCCATACTGGAGAGAGGCCTTATAAATGTTCTGAATGTGGAGAAA
GCTTCTCTCGAAGTTCACGCCTTATGAGTCACCAGAGAACTCACACAGGT

Alignment

ORF - retro_cpor_99 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.95 %
• Parental protein coverage: 66.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CLQCSKAFNHRSYLRRHQRIHTGEKPYVCSECGKAFTHCSTFILHKRAHTGEKPFKCKECGKAFSNRKDL
          C..C.K.F...S.L.RHQRIH..E......EC...F.....F.....AH.GE...KC.ECGK.FS....L
Retrocopy CPLCGKNFSNNSNLIRHQRIHAAERLCMGVECSEIFGGHPHFLSLHKAHLGEEAHKCLECGKCFSQNTHL

Parental  IRHFSIHTGEKPYECTECGKAFNRRSGLTRHQRIHSGEKPYECAECGKAFCWSTNLIRHAIIHTGEKPYK
          .RH...HTGEKPY.C..CGK.F...S.L.RHQR.H.GEKPY.C.ECG..F..S.NL.RH..IHTGE.PYK
Retrocopy TRHQRTHTGEKPYQCNVCGKSFSCNSNLHRHQRTHTGEKPYKCSECGEIFAHSSNLLRHQRIHTGERPYK

Parental  CAECGKAFSRSSSLTQHQRMHAGERPYECSQCGKSFSRTSSLIHHRRLHTGERP-YECSKCGKSFKQGSS
          CAECGK.FSRSS.L..H.R.H..ER....S..G...S..............E....ECS.CGKSF.QG..
Retrocopy CAECGKSFSRSSHLVIHERTHERERLDPFSENGEAMSDGTPFLPSQGTRRAEKKLFECSTCGKSFRQGMH

Parental  FSSHRKVHTGERPYVCEECGKTFSHSSNLRNHERVHTGERPIKCKECEKSFSCKSNLIKHLRVHTGERPY
          ...H...HTGE.PY.C..CG..FSH.SNL..H.R.HTGE.P..C.EC..SFS..SN.I.HLR.HTGERPY
Retrocopy LTRHQRTHTGEKPYKCTLCGENFSHRSNLIRHQRIHTGEKPYTCHECGDSFSHSSNRIRHLRTHTGERPY

Parental  ECSECGKSFSQSSSLIQHQRIHTG
          .CSECG.SFS.SS.L..HQR.HTG
Retrocopy KCSECGESFSRSSRLMSHQRTHTG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	6.21 RPM	1.44 RPM
SRP017611_kidney	6.49 RPM	0.84 RPM
SRP017611_liver	3.05 RPM	0.22 RPM
SRP040447_lung	6.78 RPM	1.44 RPM
SRP040447_skeletal_muscle	3.59 RPM	0.90 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_99 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_99 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000026260	1 retrocopy	retro_acar_18,
Cavia porcellus	ENSCPOG00000004610	1 retrocopy	retro_cpor_99 ,
Monodelphis domestica	ENSMODG00000023632	1 retrocopy	retro_mdom_7,